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from __future__ import absolute_import |
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import os |
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import re |
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from smartdispatch.pbs import PBS |
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from smartdispatch import utils |
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def job_generator_factory(queue, commands, prolog=[], epilog=[], command_params={}, cluster_name=None, base_path="./"): |
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if cluster_name == "guillimin": |
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return GuilliminJobGenerator(queue, commands, prolog, epilog, command_params, base_path) |
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elif cluster_name == "mammouth": |
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return MammouthJobGenerator(queue, commands, prolog, epilog, command_params, base_path) |
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elif cluster_name == "helios": |
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return HeliosJobGenerator(queue, commands, prolog, epilog, command_params, base_path) |
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elif cluster_name == "hades": |
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return HadesJobGenerator(queue, commands, prolog, epilog, command_params, base_path) |
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return JobGenerator(queue, commands, prolog, epilog, command_params, base_path) |
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class JobGenerator(object): |
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""" Offers functionalities to generate PBS files for a given queue. |
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Parameters |
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---------- |
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queue : `Queue` instance |
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queue on which commands will be executed |
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commands : list of str |
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commands to put in PBS files |
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prolog : list of str |
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code to execute before the commands |
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epilog : list of str |
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code to execute after the commands |
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command_params : dict |
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information about the commands |
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""" |
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def __init__(self, queue, commands, prolog=[], epilog=[], command_params={}, base_path="./"): |
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self.prolog = prolog |
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self.commands = commands |
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self.epilog = epilog |
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self.queue = queue |
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self.job_log_filename = '"{base_path}/logs/job/"$PBS_JOBID".{{ext}}"'.format(base_path=base_path) |
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self.nb_cores_per_command = command_params.get('nb_cores_per_command', 1) |
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self.nb_gpus_per_command = command_params.get('nb_gpus_per_command', 1) |
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self.mem_per_command = command_params.get('mem_per_command', None) |
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self.pbs_list = self._generate_base_pbs() |
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self._add_cluster_specific_rules() |
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def _add_cluster_specific_rules(self): |
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pass |
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def add_pbs_flags(self, flags): |
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resources = {} |
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options = {} |
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for flag in flags: |
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flag = flag |
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if flag.startswith('-l'): |
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resource = flag[2:] |
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split = resource.find('=') |
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resources[resource[:split]] = resource[split+1:] |
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elif flag.startswith('-'): |
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options[flag[1:2]] = flag[2:] |
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else: |
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raise ValueError("Invalid PBS flag ({})".format(flag)) |
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for pbs in self.pbs_list: |
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pbs.add_resources(**resources) |
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pbs.add_options(**options) |
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def _generate_base_pbs(self): |
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""" Generates PBS files allowing the execution of every commands on the given queue. """ |
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nb_commands_per_node = self.queue.nb_cores_per_node // self.nb_cores_per_command |
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if self.queue.nb_gpus_per_node > 0 and self.nb_gpus_per_command > 0: |
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nb_commands_per_node = min(nb_commands_per_node, self.queue.nb_gpus_per_node // self.nb_gpus_per_command) |
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# Limit number of running commands by the amount of available memory on the node. |
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if self.mem_per_command is not None: |
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nb_commands_per_node = min(nb_commands_per_node, self.queue.mem_per_node // self.mem_per_command) |
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pbs_files = [] |
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# Distribute equally the jobs among the PBS files and generate those files |
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for i, commands in enumerate(utils.chunks(self.commands, n=nb_commands_per_node)): |
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pbs = PBS(self.queue.name, self.queue.walltime) |
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# TODO Move the add_options into the JobManager once created. |
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pbs.add_options(o=self.job_log_filename.format(ext='out'), e=self.job_log_filename.format(ext='err')) |
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# Set resource: nodes |
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resource = "1:ppn={ppn}".format(ppn=len(commands) * self.nb_cores_per_command) |
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if self.queue.nb_gpus_per_node > 0: |
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resource += ":gpus={gpus}".format(gpus=len(commands) * self.nb_gpus_per_command) |
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pbs.add_resources(nodes=resource) |
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if self.mem_per_command is not None: |
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resource = "{mem}Gb".format(mem=len(commands) * self.mem_per_command) |
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pbs.add_resources(mem=resource) |
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pbs.add_modules_to_load(*self.queue.modules) |
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pbs.add_to_prolog(*self.prolog) |
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pbs.add_commands(*commands) |
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pbs.add_to_epilog(*self.epilog) |
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pbs_files.append(pbs) |
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return pbs_files |
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def write_pbs_files(self, pbs_dir="./"): |
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""" Writes PBS files allowing the execution of every commands on the given queue. |
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Parameters |
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---------- |
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pbs_dir : str |
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folder where to save pbs files |
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""" |
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pbs_filenames = [] |
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for i, pbs in enumerate(self.pbs_list): |
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pbs_filename = os.path.join(pbs_dir, 'job_commands_' + str(i) + '.sh') |
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pbs.save(pbs_filename) |
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pbs_filenames.append(pbs_filename) |
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return pbs_filenames |
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def specify_account_name_from_env(self, environment_variable_name): |
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if environment_variable_name not in os.environ: |
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raise ValueError("Undefined environment variable: ${}. Please, provide your account name!".format(environment_variable_name)) |
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account_name = os.path.basename(os.path.realpath(os.getenv(environment_variable_name))) |
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for pbs in self.pbs_list: |
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pbs.add_options(A=account_name) |
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def specify_account_name_from_file(self, rapid_filename): |
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if not os.path.isfile(rapid_filename): |
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raise ValueError("Account name file {} does not exist. Please, provide your account name!".format(rapid_filename)) |
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with open(rapid_filename, 'r') as rapid_file: |
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account_name = rapid_file.read().strip() |
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for pbs in self.pbs_list: |
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pbs.add_options(A=account_name) |
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class MammouthJobGenerator(JobGenerator): |
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def _add_cluster_specific_rules(self): |
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if self.queue.name.endswith("@mp2"): |
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for pbs in self.pbs_list: |
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pbs.resources['nodes'] = re.sub("ppn=[0-9]+", "ppn=1", pbs.resources['nodes']) |
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class HadesJobGenerator(JobGenerator): |
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def _add_cluster_specific_rules(self): |
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for pbs in self.pbs_list: |
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gpus = re.match(".*gpus=([0-9]+)", pbs.resources['nodes']).group(1) |
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pbs.resources['nodes'] = re.sub("ppn=[0-9]+", "ppn={}".format(gpus), pbs.resources['nodes']) |
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pbs.resources['nodes'] = re.sub(":gpus=[0-9]+", "", pbs.resources['nodes']) |
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class GuilliminJobGenerator(JobGenerator): |
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def _add_cluster_specific_rules(self): |
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return self.specify_account_name_from_env('HOME_GROUP') |
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# https://wiki.calculquebec.ca/w/Ex%C3%A9cuter_une_t%C3%A2che#tab=tab6 |
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class HeliosJobGenerator(JobGenerator): |
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def _add_cluster_specific_rules(self): |
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self.specify_account_name_from_file(os.path.join(os.environ['HOME'], ".default_rap")) |
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for pbs in self.pbs_list: |
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# Remove forbidden ppn option. Default is 2 cores per gpu. |
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pbs.resources['nodes'] = re.sub(":ppn=[0-9]+", "", pbs.resources['nodes']) |
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SMART-Lab /
smartdispatch
